Problem with Fracture Modifier deleting changes to mesh
In order to update the fractured mesh after making changes in Edit Mode, you either need to press the "Execute Fracture" button again, or check the "Auto Execute" checkbox so the refracture happens automatically after each change in the edit mode.

Note that depending on the mesh complexity and amount of shards the fracturing can take a bit longer, so I would recommend auto execute only on simpler meshes with less shards.